BioC 2.13: CHECK report for HTSanalyzeR on perceval

Package: HTSanalyzeR

Version: 2.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTSanalyzeR_2.14.0.tar.gz

StartedAt: 2014-04-05 02:01:41 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:08:50 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 429.2 seconds

RetCode: 0

Status:  OK

CheckDir: HTSanalyzeR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/HTSanalyzeR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSanalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSanalyzeR’ version ‘2.14.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSanalyzeR’ can be installed ... [36s/37s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘igraph’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘HTSanalyzeR/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("/////////////////////////////////////////////////////////////////////////////\n\n//------------------    Thanks for using HTSanalyzeR    -------------------//\n \n//------------please use function changes() to see new changes-------------//\n\n//------------please report any bug to xinwang2hms@gmail.com---------------//\n\n/////////////////////////////////////////////////////////////////////////////\n",     appendLF = FALSE)

See section ‘Good practice’ in '?.onAttach'.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘HTSanalyzeR-Vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [55s/57s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
GOGeneSets 5.721  0.333   6.756
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/HTSanalyzeR.Rcheck/00check.log’
for details.

* installing *source* package ‘HTSanalyzeR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HTSanalyzeR)

name	user	system	elapsed
FDRcollectionGsea	1.40	0.05	1.45
GOGeneSets	5.721	0.333	6.756
GSCA-class	0.026	0.016	0.042
HTSanalyzeR4cellHTS2	0.028	0.015	0.043
KeggGeneSets	4.230	0.130	4.441
NWA-class	0.782	0.017	0.807
aggregatePvals	0.010	0.006	0.016
analyze	0.024	0.014	0.039
analyzeGeneSetCollections	0.018	0.011	0.029
annotationConvertor	1.667	0.078	1.801
appendGSTerms	0.038	0.014	0.052
biogridDataDownload	0.003	0.003	0.006
celAnnotationConvertor	4.088	0.178	4.347
cellHTS2OutputStatTests	0.024	0.009	0.033
changes	0.003	0.003	0.006
collectionGsea	0.463	0.047	0.514
data-KcViab	1.034	0.093	1.143
drosoAnnotationConvertor	2.146	0.051	2.244
duplicateRemover	0.005	0.004	0.009
getTopGeneSets	0.045	0.013	0.058
gseaPlots	0.038	0.009	0.049
gseaScores	0.107	0.019	0.130
hyperGeoTest	4.631	0.108	4.921
interactome	0.027	0.012	0.040
mammalAnnotationConvertor	4.271	0.137	4.453
multiHyperGeoTest	0.058	0.014	0.079
networkAnalysis	0.039	0.006	0.046
networkPlot	0.037	0.007	0.048
pairwiseGsea	1.076	0.073	1.198
pairwiseGseaPlot	0.043	0.007	0.051
pairwisePhenoMannWhit	0.047	0.006	0.053
permutationPvalueCollectionGsea	1.279	0.038	1.334
plotEnrichMap	0.030	0.004	0.035
plotGSEA	0.038	0.012	0.051
plotSubNet	0.033	0.008	0.041
preprocess	0.066	0.010	0.077
report	0.035	0.009	0.047
reportAll	0.038	0.008	0.046
summarize	0.079	0.013	0.093
viewEnrichMap	0.060	0.011	0.072
viewGSEA	0.038	0.007	0.046
viewSubNet	0.044	0.006	0.050
writeReportHTSA	0.036	0.009	0.044